Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add IDR analysis #36

Open
drpatelh opened this issue Feb 12, 2019 · 2 comments
Open

Add IDR analysis #36

drpatelh opened this issue Feb 12, 2019 · 2 comments
Labels
enhancement New feature or request

Comments

@drpatelh
Copy link
Member

Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines:
https://github.com/kundajelab/atac-seq-pipeline
https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit

Another implementation in NF:
https://github.com/DoaneAS/atacflow

ENCODE ATAC-seq Guidelines:
https://www.encodeproject.org/atac-seq/

Amongst other things, this will probably also involve creating pseudo-replicates by merging and equally sampling alignments across replicates.

@drpatelh
Copy link
Member Author

As it stands bioconda::idr and bioconda::macs2 wont build in the same environment because they are built with Python 3 and Python 2, respectively.

https://anaconda.org/bioconda/idr/files

https://anaconda.org/bioconda/macs2/files

Need a workaround for this.

@ewels
Copy link
Member

ewels commented Feb 15, 2019

MACS2 Python3 support is hopefully coming... macs3-project/MACS#242 (comment) (though there have been threads around this since 2017, so not sure when..)

@drpatelh drpatelh transferred this issue from nf-core/atacseq May 30, 2019
@drpatelh drpatelh transferred this issue from nf-core/chipseq May 30, 2019
@drpatelh drpatelh added the enhancement New feature or request label Jun 26, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants